Modern DNA analytical methods and microarray technologies are potentially enabling tools for the comprehensive genetic analysis of tumors as well as premalignant lesions in patients at risk for cancer. A significant obstacle to such analysis, however, is the need for relatively large DNA samples. A recently developed isothermal whole genome amplification method promises to eliminate these barriers to comprehensive genetic analysis. This research project aims to demonstrate the utility of simple and robust amplification procedures for generating archival copies of genomic DNA from small tissue samples. Head and neck cancer will be used as a model to optimize and validate procedures for DNA archiving of neoplastic and pre-neoplastic lesions. Samples will be collected prospectively, and cancer tissue, cancer tissue margins, as well as other lesions identified as candidates for pre-neoplasia will be collected. A subset of the samples will be isolated using laser capture microdissection. All collected tissue samples and microdissected samples will be amplified to generate a DNA archive of head and neck cancer and premalignant lesion specimens. A variety of methods, including microsatellite analysis, detection of human papillomavirus subtypes, and comparative genomic hybridization (CGH) on BAC microarrays, will be used to investigate and validate the utility of the archive of amplified DNA. CGH analysis on BAC microarrays enables the detection of genetic alterations at thousands of gene loci in the archived DNA samples, which are representative of different stages of cancer, preneoplasia, or benign dysplasia. Bioinformatics tools will be used to construct alternative classification schemes based on distance-based trees or clustering algorithms, utilizing the complete data set of microsatellite, array-CGH, and HPV infection status observations. This study is intended to serve as a demonstration and validation of the utility of DNA archives, generated by isothermal whole genome amplification, for comprehensive studies in cancer genetics. The novel capabilities established by this study should be extensible to any human cancer model and should greatly expand the utilization of genetic analysis at the level of the entire genome by eliminating many of the constraints related to limited availability of biological material.